The overall goal of this Phase II project is to develop a complete system for multiplex profiling of transcription factor binding activity across a broad range of biological responses. In the Phase I SBIR, Marligen scientists demonstrated the feasibility of measuring the activities of multiple transcription factors simultaneously in a single reaction using a highly innovative, proprietary technology. In Phase II, the technology will be expanded to develop a complete system that will identify changes in the activity of 100 proteins simultaneously in one reaction. The system will comprise multiplexed bead arrays, transcription factor binding probes, assay reagents, standards and controls, and software for data analysis and interpretation. The product offering will include a broad screening panel, focused functional panels, and a modular "pick and choose" format that will offer the complete flexibility for customers to define specific arrays of their choosing. Transcription factors play a key role in controlling cellular processes. Transcription factors comprise a class of proteins central to regulating gene expression. They play a key regulatory role in controlling which genes are turned on or off in each cell, and can modulate the amount of each gene that is made. This process is both staggeringly complex and elegantly simple in design, using only a few thousand proteins to mediate an infinite variety of finely controlled processes within living organisms. The Phase II research design incorporates a strategy for screening several hundred transcription factor binding sites and adapting them to the multiplexed bead array system, development and optimization of assay reagents and procedures, biological validation in real-world research applications, and the development of a software package that will handle data analysis and visualization. The phenomenal capability of this technology to accelerate and enrich pharmaceutical research and development processes will power an unparalleled drug discovery engine, allowing scientists to better understand gene expression, more effectively unravel the pathology of diseases, and design more effective drugs. Marligen's transcription factor profiling tools will allow pharmaceutical customers to dramatically accelerate lead compound identification, preclinical drug development, and help speed the drug development pipeline.